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Video Analysis of Invertebrates’ Movement

24 Jun, 2019 @ 9:30 am 28 Jun, 2019 @ 6:00 pm

video analysis

Details

Start:
24 Jun, 2019 @ 9:30 am
End:
28 Jun, 2019 @ 6:00 pm
Cost:
€310 – €350

Palazzo Failla Hotel

via Blandini 5
Modica, 97015 Italy
+ Google Map

Outline

In this course, you will learn how to analyze the movement and behavior of invertebrates from videos. The aim is to offer you a new analytical tool to study the causes and consequences of movement in small organisms, ranging from insect to zooplankton. The course will cover all the salient aspects of video analysis, starting with basic and advanced video filming techniques (data acquisition), experimental design, and analytical pipelines for testing movement and behavior under different environmental conditions, and at population and community level. Original data will be collected and analyzed, plus a published dataset (DOI:10.4228/ZALF.DK.92) will be explored during the course. 

Themes:

  • filming techniques and video setup
  • experimental design
  • trajectory extraction with R and ImageJ (BEMOVI package)
  • data cleaning and visualization (gganimate)
  • statistical methods of movement analysis

Calendar:

Day 1:

Movement ecology and behavior:

  • Observing behavior in small organisms
  • Filming techniques
  • Introduction to R, ImageJ & ffmpeg
  • Introduction to video file formats and databases
  • Movement and morphology descriptors

Day 2:

Data acquisition:

  • Experimental design
  • Filming techniques (bright light, dark field…)
  • Find best signal-to-noise ratio
  • Trigger dramatic responses

Day 3:

Introduction to BEMOVI :

  • Video files batch conversion
  • Contrast, exposure, gamma, saturation
  • Folder structure and data input/output
  • The BEMOVI pipeline
  • Error filtering – trajectory clean-up

Day 4:

Data visualization:

  • Static vs. dynamic graphics
  • Basic and advanced trajectories visualization
  • Base R and ggplot
  • Graph animation (gganimate)
  • GIF output for data presentation

Day 5:

From code to interpretation:

  • Statistics for movement data
  • Movement parameters (speed, turning angles…)
  • HMM models (state-space models)
  • Fit a distribution

daphnia under UV stress

Trajectories of Daphnia magna under visible light (left) and UVA radiation (right). Colangeli et al. 2016.

daphnia UV test

Relevant literature:

Pennekamp et al. 2015. “BEMOVI, software for extracting behavior and morphology from videos, illustrated with analyses of microbes.” Ecology and Evolution

Colangeli et al. 2018. “Negative phototactic response to UVR in three cosmopolitan rotifers: a video analysis approach.” Hydrobiologia


Instructor:

Colangeli Pierluigi, Ph.D. @ BioMove

Hyblea Training, Italy

Topics: plankton ecology, movement and behavior analysis, biodiversity


REGISTRATION DEADLINE: 10 JUNE